Graduate Theses, Dissertations, and Problem Reports 2020 Trees, Fungi, Insects: How Host Plant Genetics Builds a Community Sandra Jeanne Simon West Virginia University, [email protected] Follow this and additional works at: https://researchrepository.wvu.edu/etd Part of the Entomology Commons, Evolution Commons, Genetics Commons, Plant Biology Commons, and the Population Biology Commons Recommended Citation Simon, Sandra Jeanne, "Trees, Fungi, Insects: How Host Plant Genetics Builds a Community" (2020). Graduate Theses, Dissertations, and Problem Reports. 7779. https://researchrepository.wvu.edu/etd/7779 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. 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Graduate Theses, Dissertations, and Problem Reports 2020 Trees, Fungi, Insects: How Host Plant Genetics Builds a Community Sandra Jeanne Simon Follow this and additional works at: https://researchrepository.wvu.edu/etd Part of the Entomology Commons, Evolution Commons, Genetics Commons, Plant Biology Commons, and the Population Biology Commons Trees, Fungi, Insects: How Host Plant Genetics Builds a Community Sandra Jeanne Simon Dissertation submitted to the Eberly College of Arts and Sciences at West Virginia University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Biology Stephen P. DiFazio, Ph.D., Chair Yong-Lak Park, Ph.D. Gina M. Wimp, Ph.D. Jonathan R. Cumming, Ph.D. Jennifer S. Hawkins, Ph.D. Morgantown, West Virginia 2020 Keywords: Populus, Salix, biotic interactions, comparative genomics, tandem duplication, community genetics, floral visitors, Andrena, phenolics, volatile organic compounds Copyright © Sandra Jeanne Simon, 2020. All rights reserved. Abstract Trees, Fungi, Insects: How Host Plant Genetics Builds a Community Sandra Jeanne Simon Organisms, such as fungi and insects, can cause millions of acres of agricultural and forest damage, while others provide billions of dollars in ecological services such as education, aesthetic enjoyment, pollination, and gardening. Plant breeding and biotechnology can potentially help establish a balance between the proliferation of detrimental pests and attraction of beneficial insects. Variation in plant physiological and morphological characteristics are extremely important in the ability of host tissues to support many different types of organisms. When that variation is genetically heritable in a plant population, shifts in the underlying genes can have predictable consequences in structuring entire ecosystems. The field of community genetics seeks to study these interactions and identify the genes important in host plants, which will ultimately allow for the prediction of community level responses to changing conditions. The main goal of my dissertation was to identify the genetic underpinnings of host plant-biotic community organization in species belonging to the Salicaceae family, which contains many species of trees and shrubs of ecological and economic importance. To date, community genetic research has established the ability of hybrid plants to have wide-ranging heritable effects on communities and ecosystems. However, only a few publications have identified the genes underlying these relationships in pure species. In chapter 2, I utilized a pseudo-backcross hybrid family of Populus and quantitative trait analysis (QTL) as well as genomic comparisons of the P. trichocarpa and P. deltoides parents to identify potential candidate genes mediating their relationship with several insect herbivores and fungal pathogens. I found that many gene candidates had undergone recent tandem duplication and this pattern was enriched relative to the rest of the genome in the native parent QTL intervals. Additionally, I found the hybrids were mediating interactions between pathogens leading to unique genetic associations that would not normally be observed in a single species population, which may contribute to the elevated community effects that have been previously observed in natural hybrid zones. In chapter 3, I used surveys that were conducted in multiple common gardens of a population of P. trichocarpa, genome wide association analysis (GWAS), and networks to identify genes and potential biological functions underlying arthropod community composition. I found that genes associated with individual arthropods appeared to be very functionally targeted with rare variants related to metabolite production and manipulation of tissue nutrition. Genes that associated with arthropod richness and community composition have biological functions that may allow them to more broadly target multiple groups of arthropods, such as terpenoid synthesis, RNA inhibition, and transmembrane protein activity. In chapter 4, I used visual observation and pan-traps to survey the tree species Salix nigra and explore the impact of dioecy on the assembly of floral insect communities. I found that male trees supported higher diversity of floral visitors on their catkins when compared to females due to visual cues of yellow pollen. I also identified the main cross-pollinators to be three species of Andrena bees, one of which (A. nigrae) showed a preference for female flowers and was correlated to specific VOC cues from catkins. Finally, I detected an asynchrony in catkin bloom and insect emergence in early spring that threatens not only the sexual reproduction of S. nigra trees, but also the survival of local A. nigrae populations. Overall, I found that the dynamic plant-pathogen- herbivore-pollinator relationships are dependent on combinations of plant genetic effects with spatial and temporal environmental variability. Acknowledgements Thank you, Steve, for all your guidance on my project and patience in helping me write this dissertation. I would never have stayed at WVU if not for your support and confidence that I would be successful in science, and I wouldn’t have been successful without you ensuring I was always well hydrated in the field and well caffeinated in the office. I also would like to thank my committee members for all your guidance and input. In particular I would like to thank Dr. Wimp for all the phone time you carved out of your schedule, whether it be normal working hours or spring break, to drop everything and talk about statistics, bugs, trees and how to find bugs on trees; Dr. Park for always being available to critique my methods and help me to improve them to capture the best version of an insect community possible for my research (and always reminding me that larvae and nymphs are not the same!); Dr. Cumming for showing me during my undergrad a look at how the experimental process develops (with an equal number of failures and successes) and sharing your knowledge of plant stress responses which helped me to structure my research; and finally Dr. Hawkins for supporting me though the Genomics Core assistantships in my final years, having one of my favorite labs in the department to collaborate with, and reminding me to fill out my defense declaration form which I am doing as I type out these acknowledgements. I would like to thank my lab including Ran Zhou, Hari Chhetri, David Macaya-Sanz, Roshan Abeyratne, and Julianne Grady. I can’t imagine a better group of people to work with in science than all of you. Also, thanks to Ryan Percifield, I learned so much about laboratory technique from you during my time in the Genomics Core it wouldn’t be a stretch to say it is one of my most valuable skill sets and an easy one to have sacrificed a lot of chocolate to acquire. Additionally, for all the people that helped me with the field and lab surveys including Dr. Jared LeBoldus, Dr. Luke Evans, Dr. Ken Keefover-Ring, Dr. William MacDonald, Dr. Nesatalu Hiese, Jacob Miller, Margo Folwick, Tanita Cheevaphantusri, and Sunita Mahat. I want to give a special shout-out to two people that I could talk to for hours about any kind of science. Ashley Henderson you have been a constant joy to work with and an even better friend through the hot mess express that is a doctorate in biology. Brandon Sinn you are easily one of the most unique and talented researchers I have had the opportunity to work closely with, I hope your career continues to inspire you the same way you did me in my last few semesters. Finally, I want to acknowledge Mark Burnham (and Maya) who has been a constant support through the end of my degree. You have helped me turn countless jumbled thoughts into many of the coherent ideas conveyed throughout this document. After my defense, I promise I will wait at least one hour after waking up before I start asking you science questions in the morning. Also, to all my co-authors for the countless hours they have spent helping collect data and edit my research chapters for final publication. Funding for this work came from the Bioenergy Science Corporation (BESC), the Center for Bioenergy Innovation